There was a time when the distance between the two sides of Lake Burley Griffin was the measure of Andrew Sayers' career move.

But the director of the National Museum of Australia, who moved there from the National Portrait Gallery three years ago, cited the tyranny of distance when he resigned from his position on Wednesday.

Mr Sayers will be just three years into his five-year term as director when he leaves to be with his wife in Melbourne.

She moved there for work two years ago and Mr Sayers told staff that ''a commuter relationship is not ideal''.

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A museum source said Mr Sayers made the shock announcement at a regular all-staff meeting and that staff were surprised.

''When he made the announcement, a ripple ran through the staff audience and there was an outburst of spontaneous applause for Andrew,'' the source said.

Mr Sayers was director of the National Portrait Gallery for 12 years before he was appointed to replace Craddock Morton as museum director in 2010.

Before the National Portrait Gallery, he worked for 13 years at the National Gallery of Australia as curator of Australian drawings, watercolours and colonial paintings and later as assistant director of collections.

Mr Sayers said in a statement that he would be leaving Canberra with ''great affection'', having worked in national cultural institutions since 1985.

''I leave the museum confident that the reputation of the museum as the home of our national treasures is one of which we can all be proud,'' he said. ''Professionally, I have enjoyed making a contribution to the museum, yet, as many couples have discovered, a 'commuter relationship' is not ideal.''

Daniel Gilbert, chairman of the museum's council, said Mr Sayers had made a significant difference to the museum during his three years there.

''He has improved its operational productivity and efficiency,''

he said. ''The museum's visitor numbers have grown and he has made changes to the look and amenity of the museum, making the visitor experience more engaging. Importantly, he has developed exhibitions from the museum's own collection.''

Mr Sayers will retire on July 1.

The news comes in the wake of recently completed negotiations regarding the Friends of the National Museum of Australia, the independent body that helped set up the museum and lobbied throughout the 1990s for a building to house the collection.

The group, which has been operating for almost 25 years, will soon cease to exist it its current form, after the members voted overwhelmingly last week to allow the museum to take over its membership and operation by June 30.

President of the group Michael Parker said although the decision had been a reluctant one, it was inevitable.

Mr Parker also paid tribute to Mr Sayers.

''We're sorry to see Andrew go - we built up a really good rapport with him,'' he said.

''Andrew was very open to our concerns and he was keen in our negotiations to reassure our membership that any future arrangements wouldn't disadvantage the membership and would bring additional advantages.''

He said Mr Sayers' legacy would be impressive and included overseeing a major building expansion program that has included displaying more of the museum's large objects in the entrance hall, a new cafe precinct and a new wing to allow for more exhibition space for the museum's growing collection.

There had also been several successful exhibitions under his directorship, including the current show to mark Canberra's Centenary, focusing on 1913, the year Canberra was officially named.